scholarly journals The structural basis of the oncogenic mutant K-Ras4B homodimers

2020 ◽  
Author(s):  
Kayra Kosoglu ◽  
Meltem Eda Omur ◽  
Hyunbum Jang ◽  
Ruth Nussinov ◽  
Ozlem Keskin ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Structural Basis ◽  
Ras Proteins ◽  
Oncogenic Ras ◽  
Extracellular Stimuli ◽  
Prediction Server ◽  
Physical Interactions ◽  
Multiple Conformations ◽  
Dynamics Simulations ◽  
Membrane Signaling

AbstractRas proteins activate their effectors through physical interactions in response to the various extracellular stimuli at the plasma membrane. Oncogenic Ras forms dimer and nanoclusters at the plasma membrane, boosting the downstream MAPK signal. It was reported that K-Ras4B can dimerize through two major interfaces: (i) the effector lobe interface, mapped to Switch I and effector binding regions; (ii) the allosteric lobe interface involving α3 and α4 helices. Recent experiments showed that constitutively active, oncogenic mutant K-Ras4BG12D dimers are enriched in the plasma membrane. Here, we perform molecular dynamics simulations of K-Ras4BG12D homodimers aiming to quantify the two major interfaces in atomic level. To examine the effect of mutations on dimerization, two double mutations, K101D/R102E on the allosteric lobe and R41E/K42D on the effector lobe interfaces were added to the K-Ras4BG12D dimer simulations. We observed that the effector lobe K-Ras4BG12D dimer is stable, while the allosteric lobe dimer alters its helical interface during the simulations, presenting multiple conformations. The K101D/R102E mutations slightly weakens the allosteric lobe interface. However, the R41E/K42D mutations disrupt the effector lobe interface. Using the homo-oligomers prediction server, we obtained trimeric, tetrameric, and pentameric complexes with the allosteric lobe K-Ras4BG12D dimers. However, the allosteric lobe dimer with the K101D/R102E mutations is not capable of generating multiple higher order structures. Our detailed interface analysis may help to develop inhibitor design targeting functional Ras dimerization and high order oligomerization at the membrane signaling platform.

scholarly journals N-terminally myristoylated Ras proteins require palmitoylation or a polybasic domain for plasma membrane localization.

1994 ◽  
Vol 14 (7) ◽  
pp. 4722-4730 ◽  
Author(s):  
K A Cadwallader ◽  
H Paterson ◽  
S G Macdonald ◽  
J F Hancock
Keyword(s):  
Plasma Membrane ◽  
Protein Kinase ◽  
Mitogen Activated Protein Kinase ◽  
Membrane Targeting ◽  
Ras Proteins ◽  
Kinase Activation ◽  
Ras Protein ◽  
Oncogenic Ras ◽  
Protein Kinase Activation ◽  
Mitogen Activated Protein

Plasma membrane targeting of Ras requires CAAX motif modifications together with a second signal from an adjacent polybasic domain or nearby cysteine palmitoylation sites. N-terminal myristoylation is known to restore membrane binding to H-ras C186S (C-186 is changed to S), a mutant protein in which all CAAX processing is abolished. We show here that myristoylated H-ras C186S is a substrate for palmitoyltransferase, despite the absence of C-terminal farnesylation, and that palmitoylation is absolutely required for plasma membrane targeting of myristoylated H-ras. Similarly, the polybasic domain is required for specific plasma membrane targeting of myristoylated K-ras. In contrast, the combination of myristoylation plus farnesylation results in the mislocalization of Ras to numerous intracellular membranes. Ras that is only myristoylated does not bind with a high affinity to any membrane. The specific targeting of Ras to the plasma membrane is therefore critically dependent on signals that are contained in the hypervariable domain but can be supported by N-terminal myristoylation or C-terminal prenylation. Interestingly, oncogenic Ras G12V that is localized correctly to the plasma membrane leads to mitogen-activated protein kinase activation irrespective of the combination of targeting signals used for localization, whereas Ras G12V that is mislocalized to the cytosol or to other membranes activates mitogen-activated protein kinase only if the Ras protein is farnesylated.

N-terminally myristoylated Ras proteins require palmitoylation or a polybasic domain for plasma membrane localization

1994 ◽  
Vol 14 (7) ◽  
pp. 4722-4730
Author(s):  
K A Cadwallader ◽  
H Paterson ◽  
S G Macdonald ◽  
J F Hancock
Keyword(s):  
Plasma Membrane ◽  
Protein Kinase ◽  
Mitogen Activated Protein Kinase ◽  
Membrane Targeting ◽  
Ras Proteins ◽  
Kinase Activation ◽  
Ras Protein ◽  
Oncogenic Ras ◽  
Protein Kinase Activation ◽  
Mitogen Activated Protein

Plasma membrane targeting of Ras requires CAAX motif modifications together with a second signal from an adjacent polybasic domain or nearby cysteine palmitoylation sites. N-terminal myristoylation is known to restore membrane binding to H-ras C186S (C-186 is changed to S), a mutant protein in which all CAAX processing is abolished. We show here that myristoylated H-ras C186S is a substrate for palmitoyltransferase, despite the absence of C-terminal farnesylation, and that palmitoylation is absolutely required for plasma membrane targeting of myristoylated H-ras. Similarly, the polybasic domain is required for specific plasma membrane targeting of myristoylated K-ras. In contrast, the combination of myristoylation plus farnesylation results in the mislocalization of Ras to numerous intracellular membranes. Ras that is only myristoylated does not bind with a high affinity to any membrane. The specific targeting of Ras to the plasma membrane is therefore critically dependent on signals that are contained in the hypervariable domain but can be supported by N-terminal myristoylation or C-terminal prenylation. Interestingly, oncogenic Ras G12V that is localized correctly to the plasma membrane leads to mitogen-activated protein kinase activation irrespective of the combination of targeting signals used for localization, whereas Ras G12V that is mislocalized to the cytosol or to other membranes activates mitogen-activated protein kinase only if the Ras protein is farnesylated.

scholarly journals Spatial diversity: Ras trafficking and signalling

2003 ◽  
Vol 25 (3) ◽  
pp. 22-24 ◽  
Author(s):  
Ian A. Prior
Keyword(s):  
Cell Proliferation ◽  
Plasma Membrane ◽  
G Proteins ◽  
Spatial Diversity ◽  
Ras Proteins ◽  
Cell Proliferation And Differentiation ◽  
Proliferation And Differentiation ◽  
Extracellular Stimuli ◽  
New Research ◽  
Ras Isoforms

Ras proteins are small monomeric G-proteins that play a central role in linking extracellular stimuli with the internal kinase cascades that are primarily involved in modulating cell proliferation and differentiation. Constitutively activated mutants of these proteins are found in many human cancers. Differences in the trafficking and plasma membrane localization of Ras isoforms play critical roles in regulating their function. New research is trying to understand the mechanisms behind, and consequences of, these differences.

scholarly journals Compartmentalization of Ras proteins

2001 ◽  
Vol 114 (9) ◽  
pp. 1603-1608 ◽  
Author(s):  
I.A. Prior ◽  
J.F. Hancock
Keyword(s):  
Plasma Membrane ◽  
Protein Interactions ◽  
Ras Proteins ◽  
Protein Protein Interactions ◽  
Diverse Range ◽  
Ras Gtpases ◽  
Extracellular Stimuli ◽  
Ras Isoforms ◽  
Complex Signaling ◽  
Exocytic Pathway

The Ras GTPases operate as molecular switches that link extracellular stimuli with a diverse range of biological outcomes. Although many studies have concentrated on the protein-protein interactions within the complex signaling cascades regulated by Ras, it is becoming clear that the spatial orientation of different Ras isoforms within the plasma membrane is also critical for their function. H-Ras, N-Ras and K-Ras use different membrane anchors to attach to the plasma membrane. Recently it has been shown that these anchors also act as trafficking signals that direct palmitoylated H-Ras and N-Ras through the exocytic pathway to the cell surface but divert polybasic K-Ras around the Golgi to the plasma membrane via an as yet-unidentified-route. Once at the plasma membrane, H-Ras and K-Ras operate in different microdomains. K-Ras is localized predominantly to the disordered plasma membrane, whereas H-Ras exists in a GTP-regulated equilibrium between disordered plasma membrane and cholesterol-rich lipid rafts. These observations provide a likely explanation for the increasing number of biological differences being identified between the otherwise highly homologous Ras isoforms and raise interesting questions about the role membrane microlocalization plays in determining the interactions of Ras with its effectors and exchange factors.

scholarly journals Plasma membrane glycosphingolipid signaling: a turning point

2021 ◽  
Author(s):  
Elena Chiricozzi
Keyword(s):  
Plasma Membrane ◽  
Chemical Synthesis ◽  
Bioinformatic Analysis ◽  
Membrane Receptors ◽  
Outer Side ◽  
Neuronal Homeostasis ◽  
Extracellular Stimuli ◽  
Conceptual Shift ◽  
Plasma Membrane Receptors ◽  
Key Events

AbstractPlasma membrane interaction is highly recognized as an essential step to start the intracellular events in response to extracellular stimuli. The ways in which these interactions take place are less clear and detailed. Over the last decade my research has focused on developing the understanding of the glycosphingolipids-protein interaction that occurs at cell surface. By using chemical synthesis and biochemical approaches we have characterized some fundamental interactions that are key events both in the immune response and in the maintenance of neuronal homeostasis. In particular, for the first time it has been demonstrated that a glycolipid, present on the outer side of the membrane, the long-chain lactosylceramide, is able to directly modulate a cytosolic protein. But the real conceptual change was the demonstration that the GM1 oligosaccharide chain is able, alone, to replicate numerous functions of GM1 ganglioside and to directly interact with plasma membrane receptors by activating specific cellular signaling. In this conceptual shift, the development and application of multidisciplinary techniques in the field of biochemistry, from chemical synthesis to bioinformatic analysis, as well as discussions with several national and international colleagues have played a key role.

scholarly journals Structural and mechanistic basis for translation inhibition by macrolide and ketolide antibiotics

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Bertrand Beckert ◽  
Elodie C. Leroy ◽  
Shanmugapriya Sothiselvam ◽  
Lars V. Bock ◽  
Maxim S. Svetlov ◽  
...  
Keyword(s):  
Antibiotic Resistance Genes ◽  
Structural Basis ◽  
Sequence Motifs ◽  
Specific Sequence ◽  
Bacterial Ribosome ◽  
Translational Arrest ◽  
Exit Tunnel ◽  
Mechanistic Basis ◽  
Dynamics Simulations ◽  
Context Specific

AbstractMacrolides and ketolides comprise a family of clinically important antibiotics that inhibit protein synthesis by binding within the exit tunnel of the bacterial ribosome. While these antibiotics are known to interrupt translation at specific sequence motifs, with ketolides predominantly stalling at Arg/Lys-X-Arg/Lys motifs and macrolides displaying a broader specificity, a structural basis for their context-specific action has been lacking. Here, we present structures of ribosomes arrested during the synthesis of an Arg-Leu-Arg sequence by the macrolide erythromycin (ERY) and the ketolide telithromycin (TEL). Together with deep mutagenesis and molecular dynamics simulations, the structures reveal how ERY and TEL interplay with the Arg-Leu-Arg motif to induce translational arrest and illuminate the basis for the less stringent sequence-specific action of ERY over TEL. Because programmed stalling at the Arg/Lys-X-Arg/Lys motifs is used to activate expression of antibiotic resistance genes, our study also provides important insights for future development of improved macrolide antibiotics.

Discovery of natural product ovalicin sensitive type 1 methionine aminopeptidases: molecular and structural basis

2019 ◽  
Vol 476 (6) ◽  
pp. 991-1003 ◽  
Author(s):  
Vijaykumar Pillalamarri ◽  
Tarun Arya ◽  
Neshatul Haque ◽  
Sandeep Chowdary Bala ◽  
Anil Kumar Marapaka ◽  
...  
Keyword(s):  
Natural Product ◽  
Active Site ◽  
Covalent Modification ◽  
Structural Basis ◽  
Wild Type ◽  
Methionine Aminopeptidases ◽  
Synthetic Derivative ◽  
Dynamics Simulations

Abstract Natural product ovalicin and its synthetic derivative TNP-470 have been extensively studied for their antiangiogenic property, and the later reached phase 3 clinical trials. They covalently modify the conserved histidine in Type 2 methionine aminopeptidases (MetAPs) at nanomolar concentrations. Even though a similar mechanism is possible in Type 1 human MetAP, it is inhibited only at millimolar concentration. In this study, we have discovered two Type 1 wild-type MetAPs (Streptococcus pneumoniae and Enterococcus faecalis) that are inhibited at low micromolar to nanomolar concentrations and established the molecular mechanism. F309 in the active site of Type 1 human MetAP (HsMetAP1b) seems to be the key to the resistance, while newly identified ovalicin sensitive Type 1 MetAPs have a methionine or isoleucine at this position. Type 2 human MetAP (HsMetAP2) also has isoleucine (I338) in the analogous position. Ovalicin inhibited F309M and F309I mutants of human MetAP1b at low micromolar concentration. Molecular dynamics simulations suggest that ovalicin is not stably placed in the active site of wild-type MetAP1b before the covalent modification. In the case of F309M mutant and human Type 2 MetAP, molecule spends more time in the active site providing time for covalent modification.

scholarly journals Ubl4A is required for insulin-induced Akt plasma membrane translocation through promotion of Arp2/3-dependent actin branching

2015 ◽  
Vol 112 (31) ◽  
pp. 9644-9649 ◽  
Author(s):  
Yu Zhao ◽  
Yuting Lin ◽  
Honghong Zhang ◽  
Adriana Mañas ◽  
Wenwen Tang ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Glycogen Synthesis ◽  
Membrane Translocation ◽  
Insulin Stimulation ◽  
Serine Threonine Kinase ◽  
Newborn Mice ◽  
Threonine Kinase ◽  
Cell Mobility ◽  
Close Proximity ◽  
Extracellular Stimuli

The serine-threonine kinase Akt is a key regulator of cell proliferation and survival, glucose metabolism, cell mobility, and tumorigenesis. Activation of Akt by extracellular stimuli such as insulin centers on the interaction of Akt with PIP3 on the plasma membrane, where it is subsequently phosphorylated and activated by upstream protein kinases. However, it is not known how Akt is recruited to the plasma membrane upon stimulation. Here we report that ubiquitin-like protein 4A (Ubl4A) plays a crucial role in insulin-induced Akt plasma membrane translocation. Ubl4A knockout newborn mice have defective Akt-dependent glycogen synthesis and increased neonatal mortality. Loss of Ubl4A results in the impairment of insulin-induced Akt translocation to the plasma membrane and activation. Akt binds actin-filaments and colocalizes with actin-related protein 2 and 3 (Arp2/3) complex in the membrane ruffles and lamellipodia. Ubl4A directly interacts with Arp2/3 to accelerate actin branching and networking, allowing Akt to be in close proximity to the plasma membrane for activation upon insulin stimulation. Our finding reveals a new mechanism by which Akt is recruited to the plasma membrane for activation, thereby providing a missing link in Akt signaling.

The COOH-terminal domain of the Rap1A (Krev-1) protein is isoprenylated and supports transformation by an H-Ras:Rap1A chimeric protein

1991 ◽  
Vol 11 (3) ◽  
pp. 1523-1530
Author(s):  
J E Buss ◽  
L A Quilliam ◽  
K Kato ◽  
P J Casey ◽  
P A Solski ◽  
...  
Keyword(s):  
Biological Activities ◽  
Chimeric Protein ◽  
Cell System ◽  
Full Length ◽  
Ras Proteins ◽  
3T3 Cells ◽  
Farnesyl Transferase ◽  
Oncogenic Ras ◽  
Nih 3T3 ◽  
Nih 3T3 Cells

Although the Rap1A protein resembles the oncogenic Ras proteins both structurally and biochemically, Rap1A exhibits no oncogenic properties. Rather, overexpression of Rap1A can reverse Ras-induced transformation of NIH 3T3 cells. Because the greatest divergence in amino acid sequence between Ras and Rap1A occurs at the COOH terminus, the role of this domain in the opposing biological activities of these proteins was examined. COOH-terminal processing and membrane association of Rap1A were studied by constructing and expressing a chimeric protein (composed of residues 1 to 110 of an H-Ras activated by a Leu-61 mutation attached to residues 111 to 184 of Rap1A) in NIH 3T3 cells and a full-length human Rap1A protein in a baculovirus-Sf9 insect cell system. Both the chimeric protein and the full-length protein were synthesized as a 23-kDa cytosolic precursor that rapidly bound to membranes and was converted into a 22-kDa form that incorporated label derived from [3H]mevalonate. The mature 22-kDa form also contained a COOH-terminal methyl group. Full-length Rap1A, expressed in insect cells, was modified by a C20 (geranylgeranyl) isoprenoid. In contrast, H-Ras, expressed in either Sf9 insect or NIH 3T3 mouse cells contained a C15 (farnesyl) group. This suggests that the Rap1A COOH terminus is modified by a prenyl transferase that is distinct from the farnesyl transferase that modifies Ras proteins. Nevertheless, in NIH 3T3 cells the chimeric Ras:Rap1A protein retained the transforming activity conferred by the NH2-terminal Ras61L domain. This demonstrates that the modifications and localization signals of the COOH terminus of Rap1A can support the interactions between H-Ras and membranes that are required for transformation.

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